MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq

Single-cell DNA template strand sequencing (Strand-seq) allows a range of various genomic analysis including chromosome length haplotype phasing and structural variation (SV) calling in individual cells. Here, we present MosaiCatcher v2, a standardised workflow and reference framework for single-cell SV detection using Strand-seq. This framework introduces a range of functionalities, including: an automated upstream Quality Control (QC) and assembly sub-workflow that relies on multiple genome assemblies and incorporates a multistep normalisation module, integration of the scNOVA SV functional characterization and of the ArbiGent SV genotyping modules, platform portability, as well as a user-friendly and shareable web report. These new features of MosaiCatcher v2 enables reproducible computational processing of Strand-seq data, which are increasingly used in human genetics and single cell genomics, towards production environments. Availability and ImplementationMosaicatcher v2 is a standardised workflow, implemented using the Snakemake workflow management system. The pipeline is available on GitHub: https://github.com/friendsofstrandseq/mosaicatcher-pipeline/ and on the snakemake-workflow-catalog: https://snakemake.github.io/snakemake-workflow-catalog/?usage=friendsofstrandseq/mosaicatcher-pipeline. Contactjan.korbel@embl.de Supplementary informationSupplementary data are available at Bioinformatics online.